Writing and modifying attributes to h5 files

I have a *.h5 file with two groups - '/info' and '/data'. The '/info' group contains a series of 14 attributes that provide relevant information about the datasets in '/data'. I want to develop an 'attribute editor' for the '/info' attributes, but I am having difficultly modifying the existing attributes. I have tried two approaches using hdf5write and h5attput (from hdf5tools on matlab central).

Using hdf5write I can do the following:

    attr = ‘new_info';
    attr_details.Name = 'New_Attribute';
    attr_details.AttachedTo = '/info’;
    attr_details.AttachType = 'group';
    hdf5write('myh5file.h5',attr_details, attr, 'WriteMode', 'append');

If the attribute didn’t exist previously, this seems to work fine – I get a new attribute ‘/info/New_Attribute’ whose Value.Data = ’new_info’. However, if I decide that I want to change this by continuing with

    attr = ‘newer_info';
    hdf5write('myh5file.h5',attr_details, attr, 'WriteMode', 'append');

I get the error

    ??? Error using ==> hdf5writec
    writeH5Attr: Couldn't create attribute.

    Error in ==> hdf5write at 143
    hdf5writec(file, details, varargin{dset_idx});

Changing the ‘WriteMode’ to ‘overwrite’ doesn’t work either.

Using h5attput is similar, as I can create a new attribute with the command

    h5attput('myh5file.h5','/info','New_Attribute','new_info’);

but trying to modify ‘New_Attribute’ gives an error, i.e.

    h5attput('myh5file.h5','/info','New_Attribute','newer_info’);

    ??? Error using ==> hdf5lib2
    The HDF5 library encountered an error:  "Unknown error."

    Error in ==> write at 36
    H5ML.hdf5lib2('H5Awrite', varargin{:});

    Error in ==> h5attput at 51
    H5A.write(att_id,datatype_id,attvalue);

The difference with h5attput is that for numeric data, I am able to modify the attributes, so for example:

    h5attput('myh5file.h5','/info','Numeric_Attribute',12);

creates the attribute ‘/info/Numeric_Attribute’ with Value = 12, which can be updated successfully with something like:

    h5attput('myh5file.h5','/info','Numeric_Attribute',58);

So, in summary, I can use hdf5write or h5attput to create new attributes within an existing group, but I cannot modify the attributes using commands similar to those used to create them. The exception is using h5attput in the case where the attribute has a numeric value. I have also tried creating an h5 string object

    new_info = hdf5.h5string('new_info’)

but neither hdf5write or h5attput accepts the h5 string as an input.

Thanks in advance for any input and ideas.

Answer 1

[Ashish Uthama]

HDF5 attributes cannot be 'overwritten' with a different datatype.

Since both the functions you mention work for you in creating attributes, one approach would be to delete the attribute iff it already exists and then create a new one.

Here is a snippet showing how to delete an existing attribute:

    h5file        = 'myfile.h5';
    location      = '/info';
    attributeName = 'Some_Attribute';
    % Open the file (ensure to close it automatically when done)
    fileID = H5F.open(h5file,'H5F_ACC_RDWR','H5P_DEFAULT');
    fileIDCleanUp = onCleanup(@()H5F.close(fileID));
    % Open the dataset/group
    locID  = H5O.open(fileID, location,'H5P_DEFAULT');
    locIDCleanUp = onCleanup(@()H5O.close(locID));
    try %to open the attribute.
       attID = H5A.open(locID, attributeName, 'H5P_DEFAULT');
       H5A.close(attID);
       H5A.delete(locID, attributeName);
    catch ALL
        % do nothing if the attribute does not exist.
    end